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        <a href="BIP.SDE-module.html">Package&nbsp;SDE</a> ::
        Module&nbsp;gillespie
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<h1 class="epydoc">Source Code for <a href="BIP.SDE.gillespie-module.html">Module BIP.SDE.gillespie</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># -*- coding:utf-8 -*-</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"># Name:        gillespie.py</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"># Project:      Bayesian-Inference</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment"># Purpose:     </tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"># Author:      Fl&#225;vio Code&#231;o Coelho&lt;fccoelho@gmail.com&gt;</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment"># Created:     2008-11-26</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment"># Copyright:   (c) 2008 by the Author</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-comment"># Licence:     GPL</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-docstring">"restructuredtext en"</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">random</tt> <tt class="py-keyword">import</tt> <tt class="py-name">uniform</tt><tt class="py-op">,</tt> <tt class="py-name">multinomial</tt><tt class="py-op">,</tt> <tt class="py-name">exponential</tt><tt class="py-op">,</tt><tt class="py-name">random</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">arange</tt><tt class="py-op">,</tt> <tt class="py-name">array</tt><tt class="py-op">,</tt> <tt class="py-name">empty</tt><tt class="py-op">,</tt><tt class="py-name">zeros</tt><tt class="py-op">,</tt><tt class="py-name">log</tt><tt class="py-op">,</tt> <tt class="py-name">isnan</tt><tt class="py-op">,</tt> <tt class="py-name">nanmax</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">time</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">copy</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">multiprocessing</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Pool</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package BIP=BIP-module.html"><a title="BIP" class="py-name" href="#" onclick="return doclink('link-0', 'BIP', 'link-0');">BIP</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Variable BIP.Bayes.Melding.Viz=BIP.Bayes.Melding-module.html#Viz,Package BIP.Viz=BIP.Viz-module.html"><a title="BIP.Bayes.Melding.Viz
BIP.Viz" class="py-name" href="#" onclick="return doclink('link-1', 'Viz', 'link-1');">Viz</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module BIP.Viz.realtime=BIP.Viz.realtime-module.html"><a title="BIP.Viz.realtime" class="py-name" href="#" onclick="return doclink('link-2', 'realtime', 'link-2');">realtime</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class BIP.Viz.realtime.RTplot=BIP.Viz.realtime.RTplot-class.html"><a title="BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-3', 'RTplot', 'link-3');">RTplot</a></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">    <tt id="link-4" class="py-name" targets="Variable BIP.SDE.gillespie.ser=BIP.SDE.gillespie-module.html#ser"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-4', 'ser', 'link-4');">ser</a></tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="BIP.Viz.realtime.RTplot" class="py-name" href="#" onclick="return doclink('link-5', 'RTplot', 'link-3');">RTplot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">    <tt id="link-6" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-6', 'ser', 'link-4');">ser</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">psyco</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">    <tt class="py-name">psyco</tt><tt class="py-op">.</tt><tt class="py-name">full</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-keyword">pass</tt> </tt>
<a name="dispatch"></a><div id="dispatch-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="dispatch-toggle" onclick="return toggle('dispatch');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.gillespie-module.html#dispatch">dispatch</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="dispatch-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="dispatch-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">    <tt class="py-docstring">'''this function is necessary for paralelization'''</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">    <tt id="link-7" class="py-name" targets="Function BIP.Bayes.Melding.model()=BIP.Bayes.Melding-module.html#model"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-7', 'model', 'link-7');">model</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-8', 'ser', 'link-4');">ser</a></tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-9', 'ser', 'link-4');">ser</a></tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-10" class="py-name"><a title="BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-10', 'model', 'link-7');">model</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method BIP.SDE.gillespie.Model.GSSA()=BIP.SDE.gillespie.Model-class.html#GSSA"><a title="BIP.SDE.gillespie.Model.GSSA" class="py-name" href="#" onclick="return doclink('link-11', 'GSSA', 'link-11');">GSSA</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"> </tt>
<a name="Model"></a><div id="Model-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="Model-toggle" onclick="return toggle('Model');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BIP.SDE.gillespie.Model-class.html">Model</a><tt class="py-op">:</tt> </tt>
</div><div id="Model-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Model-expanded"><a name="Model.__init__"></a><div id="Model.__init__-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="Model.__init__-toggle" onclick="return toggle('Model.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.gillespie.Model-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">vnames</tt><tt class="py-op">,</tt><tt class="py-param">rates</tt><tt class="py-op">,</tt><tt class="py-param">inits</tt><tt class="py-op">,</tt> <tt class="py-param">tmat</tt><tt class="py-op">,</tt><tt class="py-param">propensity</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Model.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Model.__init__-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-docstring">         * vnames: list of strings</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-docstring">         * rates: list of fixed rate parameters</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-docstring">         * inits: list of initial values of variables</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-docstring">         * propensity: list of lambda functions of the form: </tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-docstring">            lambda r,ini: some function of rates ans inits.</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">vn</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name" targets="Variable BIP.SDE.example.vnames=BIP.SDE.example-module.html#vnames"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-12', 'vnames', 'link-12');">vnames</a></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rates</tt> <tt class="py-op">=</tt> <tt class="py-name">rates</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt> <tt class="py-op">=</tt> <tt class="py-name">inits</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tm</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name" targets="Variable BIP.SDE.example.tmat=BIP.SDE.example-module.html#tmat"><a title="BIP.SDE.example.tmat" class="py-name" href="#" onclick="return doclink('link-13', 'tmat', 'link-13');">tmat</a></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pv</tt> <tt class="py-op">=</tt> <tt class="py-name">propensity</tt><tt class="py-comment">#[compile(eq,'errmsg','eval') for eq in propensity]</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pvl</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pv</tt><tt class="py-op">)</tt> <tt class="py-comment">#length of propensity vector</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pv0</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pvl</tt><tt class="py-op">,</tt><tt class="py-name">dtype</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nvars</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt><tt class="py-op">)</tt> <tt class="py-comment">#number of variables</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">time</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tmax</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">steps</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">viz</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> <tt class="py-comment">#if intermediate vizualization should be on</tt> </tt>
</div><a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">         </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">     </tt>
<a name="Model.getStats"></a><div id="Model.getStats-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="Model.getStats-toggle" onclick="return toggle('Model.getStats');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.gillespie.Model-class.html#getStats">getStats</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Model.getStats-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Model.getStats-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">steps</tt> </tt>
</div><a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">     </tt>
<a name="Model.run"></a><div id="Model.run-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="Model.run-toggle" onclick="return toggle('Model.run');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.gillespie.Model-class.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">method</tt><tt class="py-op">=</tt><tt class="py-string">'SSA'</tt><tt class="py-op">,</tt> <tt class="py-param">tmax</tt><tt class="py-op">=</tt><tt class="py-number">10</tt><tt class="py-op">,</tt> <tt class="py-param">reps</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">viz</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">serial</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Model.run-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Model.run-expanded"><a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-docstring">        Runs the model.</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring">            - `method`: String specifying the solving algorithm. Currently only 'SSA'</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">            - `tmax`: duration of the simulation.</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">            - `reps`: Number of replicates.</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">            - `viz`: Boolean. Whether to show graph of each replicate during simulation</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">            - `serial`: Boolean. False to run replicate in parallel when more than one core is a vailable. True to run them serially (easier to debug).</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring">        :Return:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">            a numpy array of shape (reps,tmax,nvars)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-14" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-14', 'ser', 'link-4');">ser</a></tt><tt class="py-op">:</tt> <tt class="py-comment">#only if Gnuplot.py is installed</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">viz</tt> <tt class="py-op">=</tt> <tt class="py-name">viz</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tmax</tt> <tt class="py-op">=</tt> <tt class="py-name">tmax</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">        <tt class="py-comment">#self.res = zeros((tmax,self.nvars,reps),dtype=float)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">tmax</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nvars</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">dtype</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">        <tt class="py-name">tvec</tt> <tt class="py-op">=</tt> <tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">tmax</tt><tt class="py-op">,</tt> <tt class="py-name">dtype</tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">             </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt><tt class="py-string">'SSA'</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">serial</tt><tt class="py-op">:</tt><tt class="py-comment"># Parallel version</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">                <tt class="py-name">pool</tt> <tt class="py-op">=</tt> <tt class="py-name">Pool</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">pool</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt id="link-15" class="py-name" targets="Function BIP.SDE.gillespie.dispatch()=BIP.SDE.gillespie-module.html#dispatch"><a title="BIP.SDE.gillespie.dispatch" class="py-name" href="#" onclick="return doclink('link-15', 'dispatch', 'link-15');">dispatch</a></tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">reps</tt><tt class="py-op">,</tt> <tt class="py-name">chunksize</tt><tt class="py-op">=</tt><tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">                <tt class="py-name">pool</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">                <tt class="py-name">pool</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">                <tt class="py-keyword">print</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">steps</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt><tt class="py-comment"># Serial</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="BIP.SDE.gillespie.dispatch" class="py-name" href="#" onclick="return doclink('link-16', 'dispatch', 'link-15');">dispatch</a></tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">reps</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">             </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">method</tt> <tt class="py-op">==</tt> <tt class="py-string">'SSAct'</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">         </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">time</tt> <tt class="py-op">=</tt> <tt class="py-name">tvec</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">series</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> </tt>
</div><a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt class="py-comment">#self.steps=steps</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">     </tt>
<a name="Model.GSSA"></a><div id="Model.GSSA-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="Model.GSSA-toggle" onclick="return toggle('Model.GSSA');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.gillespie.Model-class.html#GSSA">GSSA</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Model.GSSA-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Model.GSSA-expanded"><a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-docstring">        Gillespie Direct algorithm</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-name">tmax</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tmax</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">        <tt id="link-17" class="py-name" targets="Variable BIP.SDE.example.ini=BIP.SDE.example-module.html#ini"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-17', 'ini', 'link-17');">ini</a></tt> <tt class="py-op">=</tt> <tt class="py-name">copy</tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inits</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">        <tt id="link-18" class="py-name" targets="Variable BIP.SDE.example.r=BIP.SDE.example-module.html#r"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-18', 'r', 'link-18');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rates</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt class="py-name">pvi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pv</tt> <tt class="py-comment">#propensity functions</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">        <tt class="py-name">tm</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tm</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-name">pv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pv0</tt> <tt class="py-comment">#actual propensity values for each time step</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-name">tc</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">steps</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-19', 'ini', 'link-17');">ini</a></tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">tim</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">tmax</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-name">tc</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">tim</tt><tt class="py-op">:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">                <tt class="py-name">i</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">                <tt class="py-name">a0</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pvi</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">                    <tt class="py-name">pv</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-20', 'r', 'link-18');">r</a></tt><tt class="py-op">,</tt><tt id="link-21" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-21', 'ini', 'link-17');">ini</a></tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">                    <tt class="py-name">a0</tt><tt class="py-op">+=</tt><tt class="py-name">pv</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">                    <tt class="py-name">i</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">                <tt class="py-name">tau</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">/</tt><tt class="py-name">a0</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">pv</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-comment">#no change in state is pv is all zeros</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">                    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">                        <tt class="py-name">event</tt> <tt class="py-op">=</tt> <tt class="py-name">multinomial</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">pv</tt><tt class="py-op">/</tt><tt class="py-name">a0</tt><tt class="py-op">)</tt> <tt class="py-comment"># event which will happen on this iteration</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">                    <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt><tt class="py-comment"># as inst:#2.6 syntax</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">                        <tt class="py-comment">#print inst</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">                        <tt class="py-keyword">print</tt> <tt class="py-string">"pv: "</tt><tt class="py-op">,</tt><tt class="py-name">pv</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">                        <tt class="py-keyword">print</tt> <tt class="py-string">"Rates: "</tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-22', 'r', 'link-18');">r</a></tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">                        <tt class="py-keyword">print</tt> <tt class="py-string">"State: "</tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-23', 'ini', 'link-17');">ini</a></tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">                        <tt class="py-keyword">print</tt> <tt class="py-string">"Time Step: "</tt><tt class="py-op">,</tt><tt class="py-name">tim</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">                        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">                    <tt id="link-24" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-24', 'ini', 'link-17');">ini</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">tm</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">nonzero</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">                <tt class="py-comment">#print tc, ini</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">                <tt class="py-name">tc</tt> <tt class="py-op">+=</tt> <tt class="py-name">tau</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">steps</tt> <tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">a0</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-keyword">break</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">[</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-25', 'ini', 'link-17');">ini</a></tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-comment">#            if a0 == 0: break</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">viz</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-26', 'ser', 'link-4');">ser</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method BIP.Viz.realtime.RTplot.clearFig()=BIP.Viz.realtime.RTplot-class.html#clearFig"><a title="BIP.Viz.realtime.RTplot.clearFig" class="py-name" href="#" onclick="return doclink('link-27', 'clearFig', 'link-27');">clearFig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-28', 'ser', 'link-4');">ser</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method BIP.Viz.realtime.RTplot.plotlines()=BIP.Viz.realtime.RTplot-class.html#plotlines"><a title="BIP.Viz.realtime.RTplot.plotlines" class="py-name" href="#" onclick="return doclink('link-29', 'plotlines', 'link-29');">plotlines</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-name">names</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">vn</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> </tt>
</div></div><a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"> </tt>
<a name="p1"></a><div id="p1-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="p1-toggle" onclick="return toggle('p1');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.gillespie-module.html#p1">p1</a><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">,</tt><tt class="py-param">ini</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt id="link-30" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-30', 'r', 'link-18');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt id="link-31" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-31', 'ini', 'link-17');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt id="link-32" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-32', 'ini', 'link-17');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div><a name="p2"></a><div id="p2-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="p2-toggle" onclick="return toggle('p2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.gillespie-module.html#p2">p2</a><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">,</tt><tt class="py-param">ini</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt id="link-33" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-33', 'r', 'link-18');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt id="link-34" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-34', 'ini', 'link-17');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div><a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"> </tt>
<a name="main"></a><div id="main-def"><a name="L147"></a><tt class="py-lineno">147</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.gillespie-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="main-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="main-expanded"><a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">    <tt id="link-35" class="py-name"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-35', 'vnames', 'link-12');">vnames</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt><tt class="py-string">'I'</tt><tt class="py-op">,</tt><tt class="py-string">'R'</tt><tt class="py-op">]</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">    <tt id="link-36" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-36', 'ini', 'link-17');">ini</a></tt><tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">500</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">    <tt class="py-name">rates</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">.001</tt><tt class="py-op">,</tt><tt class="py-number">.1</tt><tt class="py-op">]</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt class="py-name">tm</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">    <tt class="py-comment">#prop=[lambda r, ini:r[0]*ini[0]*ini[1],lambda r,ini:r[0]*ini[1]]</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">    <tt id="link-37" class="py-name" targets="Variable BIP.SDE.example.M=BIP.SDE.example-module.html#M"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-37', 'M', 'link-37');">M</a></tt> <tt class="py-op">=</tt> <tt id="link-38" class="py-name" targets="Class BIP.SDE.gillespie.Model=BIP.SDE.gillespie.Model-class.html,Class BIP.SMC.condensation.Model=BIP.SMC.condensation.Model-class.html"><a title="BIP.SDE.gillespie.Model
BIP.SMC.condensation.Model" class="py-name" href="#" onclick="return doclink('link-38', 'Model', 'link-38');">Model</a></tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-39', 'vnames', 'link-12');">vnames</a></tt> <tt class="py-op">=</tt> <tt id="link-40" class="py-name"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-40', 'vnames', 'link-12');">vnames</a></tt><tt class="py-op">,</tt><tt class="py-name">rates</tt> <tt class="py-op">=</tt> <tt class="py-name">rates</tt><tt class="py-op">,</tt><tt class="py-name">inits</tt><tt class="py-op">=</tt><tt id="link-41" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-41', 'ini', 'link-17');">ini</a></tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name"><a title="BIP.SDE.example.tmat" class="py-name" href="#" onclick="return doclink('link-42', 'tmat', 'link-13');">tmat</a></tt><tt class="py-op">=</tt><tt class="py-name">tm</tt><tt class="py-op">,</tt><tt class="py-name">propensity</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt id="link-43" class="py-name" targets="Function BIP.SDE.gillespie.p1()=BIP.SDE.gillespie-module.html#p1"><a title="BIP.SDE.gillespie.p1" class="py-name" href="#" onclick="return doclink('link-43', 'p1', 'link-43');">p1</a></tt><tt class="py-op">,</tt><tt id="link-44" class="py-name" targets="Function BIP.SDE.gillespie.p2()=BIP.SDE.gillespie-module.html#p2"><a title="BIP.SDE.gillespie.p2" class="py-name" href="#" onclick="return doclink('link-44', 'p2', 'link-44');">p2</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">    <tt id="link-45" class="py-name" targets="Variable BIP.SDE.example.t0=BIP.SDE.example-module.html#t0"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-45', 't0', 'link-45');">t0</a></tt><tt class="py-op">=</tt><tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">    <tt id="link-46" class="py-name"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-46', 'M', 'link-37');">M</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method BIP.Bayes.Melding.FitModel.run()=BIP.Bayes.Melding.FitModel-class.html#run,Method BIP.Bayes.Melding.Meld.run()=BIP.Bayes.Melding.Meld-class.html#run,Method BIP.SDE.gillespie.Model.run()=BIP.SDE.gillespie.Model-class.html#run"><a title="BIP.Bayes.Melding.FitModel.run
BIP.Bayes.Melding.Meld.run
BIP.SDE.gillespie.Model.run" class="py-name" href="#" onclick="return doclink('link-47', 'run', 'link-47');">run</a></tt><tt class="py-op">(</tt><tt class="py-name">tmax</tt><tt class="py-op">=</tt><tt class="py-number">80</tt><tt class="py-op">,</tt><tt class="py-name">reps</tt><tt class="py-op">=</tt><tt class="py-number">100</tt><tt class="py-op">,</tt><tt class="py-name">viz</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt><tt class="py-name">serial</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-string">'total time: '</tt><tt class="py-op">,</tt><tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-48" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-48', 't0', 'link-45');">t0</a></tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">    <tt class="py-comment">#print res</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">    <tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">steps</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-49', 'M', 'link-37');">M</a></tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method BIP.SDE.gillespie.Model.getStats()=BIP.SDE.gillespie.Model-class.html#getStats"><a title="BIP.SDE.gillespie.Model.getStats" class="py-name" href="#" onclick="return doclink('link-50', 'getStats', 'link-50');">getStats</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">    <tt id="link-51" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-51', 'ser', 'link-4');">ser</a></tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt class="py-name">pylab</tt> <tt class="py-keyword">import</tt> <tt class="py-name">plot</tt> <tt class="py-op">,</tt> <tt class="py-name">show</tt><tt class="py-op">,</tt> <tt class="py-name">legend</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">    <tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt id="link-52" class="py-name"><a title="BIP.SDE.gillespie.ser" class="py-name" href="#" onclick="return doclink('link-52', 'ser', 'link-4');">ser</a></tt><tt class="py-op">,</tt><tt class="py-string">'-.'</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">    <tt class="py-name">legend</tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-53', 'M', 'link-37');">M</a></tt><tt class="py-op">.</tt><tt class="py-name">vn</tt><tt class="py-op">,</tt><tt class="py-name">loc</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">    <tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">     </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt><tt class="py-op">==</tt><tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">    <tt class="py-comment">#import cProfile</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">    <tt class="py-comment">#cProfile.run('main()',sort=1,filename='gillespie.profile')</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">    <tt id="link-54" class="py-name" targets="Function BIP.SDE.gillespie.main()=BIP.SDE.gillespie-module.html#main"><a title="BIP.SDE.gillespie.main" class="py-name" href="#" onclick="return doclink('link-54', 'main', 'link-54');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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